GSM7925858: Ctrl1_ATAC; Mus musculus; ATAC-seq
For ATAC-seq, the extracted nuclei were re-suspended fragmented buffer including 1.5 μL transposome (novoprotein N248), and incubated at 37 oC for 30 min. For CUT&Tag, cells were sorted enriched by ConA-magnetic beads, and then incubated overnight with antibody. The next day, beads were washed and incubated with anti-rabbit secondary antibody. Then the beads were washed and incubated with proteinA/G-Tnp transposome in Chitag. Next, cells were resuspended in 100 μL Tagmentation buffer (10 mM MgCl in Chitag Buffer) and incubated at 37 °C for 1 hr. The tagmentation was terminated by adding 1 μL of 10% SDS at 55 °C for 10 min. For HiC, the sorted cells were crosslinked with 1% formaldehyde and lysed in 1 ml lysis buffer. The resulting chromatin was then digested with NUB I (NEB) restriction enzymes at at 37 °C overnight. The DNA ends were blunted and labelled with biotin by Klenow DNA polymerase, followed by ligation using T4 DNA ligase (NEB). After reverse crosslinking, DNA was fragmented by sonication. For ATAC-seq, the products were purified with tagment DNA extract beads (novoprotein N245), and then amplified by PCR for 14 cycles with NovoNGS index kit for illumine (N239). For CUT&Tag, the DNA fragments added 1 μL spike in (Vazyme) and were extracted by DNA extract beads, then amplified by PCR for 12 cycles with TruePrep index kit for illumine. For HiC, the DNA fragments were then end-repaired and the biotinylated DNA fragments were captured using Dynabeads MyOne Streptavidin C1 beads (Invitrogen, Termo Fisher Scientifc). The DNA on beads was ligated to the Truseq adaptors and amplifed with PCR for library construction.